inst/report_motif_matches.md

In philliplab/MotifBinner: Bin reads by Motif

Motif Searches

Sys.time()

## [1] "2015-03-19 13:09:27 SAST"

Input parameters for the searches

print(prefix)

## [1] "CCAGCTGGTTATGCGATTCTMARGTG"

print(suffix)

## [1] "CTGAGCGTGTGGCAAGGCCC"

print(motif_length)

## [1] 9

Matched vs Unmatched sequences

n_matched <- length(motif_dat$matched_seq)
n_unmatched <- length(motif_dat$unmatched_seq)
n_total <- n_matched + n_unmatched
kable(data.frame(seq_matched_count = n_matched,
                 seq_matched_perc = 100*round(n_matched / n_total, 4),
                 seq_unmatched_count = n_unmatched,
                 seq_unmatched_perc = 100*round(n_unmatched / n_total, 4)))

| seq_matched_count| seq_matched_perc| seq_unmatched_count| seq_unmatched_perc| |-----------------:|----------------:|-------------------:|------------------:| | 11561| 79.32| 3014| 20.68|

Matched Sequences

Summary of sequences

print(motif_dat$matched_seq)

##   A DNAStringSet instance of length 11561
##         width seq                                      names               
##     [1]   299 TATGGGATCAAAGTCTAAA...CCTATACATTATTGTGCT CTTACCTAA
##     [2]   299 TATGGGACGAAAGCCTCAA...CCTATACATTATTGTGCT TTAGATGTT
##     [3]   308 TATGGGACGAAAGTCTAAA...CCTATACATTATTGTGCT TATTGGGGC
##     [4]   299 TATGGGACGAAAGCCTCAA...CCTATACATTATTGTGCT ATTGTGCCA
##     [5]   299 TATGGGATGAAAGCCTCAA...CCTATACATTATTGTGCT GTAGACTGT
##     ...   ... ...
## [11557]   299 TATGGGACGAAAGTCTAAA...CCTATACATTATTGTGCT GTACACAAG
## [11558]   299 TATGGGACGAAAGCCTCAA...CCTATACATTATTGTGCT CATTTAAAA
## [11559]   299 TATGGGACGAAAGTCTCAA...CCTATACATTATTGTGCT GCTCAAGTA
## [11560]   308 TATGGGATCAAAGTCTAAA...CCTATACATTATTGTGCT AATCCTCTA
## [11561]   299 TATGGGACGAAAGTCTAAA...CCTATACATTATGGTGCT TAATTGCGA

The letter frequencies

Counts of the letters in the matched sequences.

x <- apply(consensusMatrix(motif_dat$matched_seq), 1, sum)
x <- x[x != 0]
kable(data.frame(letter = names(x),
                 count = x,
                 count_per_seq = round(x/length(motif_dat$matched_seq),2),
                 row.names = 1:length(x)))

|letter | count| count_per_seq| |:------|-------:|-------------:| |A | 1296178| 112.12| |C | 675110| 58.40| |G | 536220| 46.38| |T | 978310| 84.62| |+ | 2| 0.00|

Normalized counts of the letters in the matched sequences.

x_freq <- round(x/sum(x), 4)
kable(data.frame(letter = names(x_freq),
                 count = x_freq,
                 row.names = 1:length(x_freq)))

|letter | count| |:------|------:| |A | 0.3718| |C | 0.1937| |G | 0.1538| |T | 0.2807| |+ | 0.0000|

barplot(x/sum(x),
        main = 'Normalized counts of the letters\nin the matched sequences')

The sequence lengths

hist(width(motif_dat$matched_seq),
     main = "Histogram of the lengths of the matched sequences",
     xlab = "Sequence Length",
     ylab = "Number of Sequences")

Unmatched Sequences

Summary of sequences

print(motif_dat$unmatched_seq)

##   A DNAStringSet instance of length 3014
##        width seq                                       names               
##    [1]   419 AATGTCAGCACAGTACAAT...CCTGAGCGTGTGGCAAGGC seq_4
##    [2]   351 TATGGGACCAAAGTCTAAA...ACTGAGCGTGTGGCAAGGC seq_5
##    [3]   353 TATGGGACGAAAGCCTCAA...CCTGAGCGTGTGGCAAGGC seq_10
##    [4]   351 TATGGGACGAAAGCCTCAA...CCTGAGCGTGTGGCAAGGC seq_15
##    [5]   343 TATGGGATGAAAGCCTAAA...CCTGAGCGTGTGGCAAGGC seq_17
##    ...   ... ...
## [3010]   419 AATGTCAGTACAGTACAAT...ACTGAGCGTGTGGCAAGGC seq_14561
## [3011]   419 AATGTCAGTACAGTACAAT...ACTGAGCGTGTGGCAAGGC seq_14562
## [3012]   418 AATGTCAGTACAGTACAAT...CCTGAGCGTGTGGCAAGGC seq_14563
## [3013]   419 AATGTAAGCACAGTACAAT...CCTGAGCGTGTGGCAAGGC seq_14564
## [3014]   419 AATGTCAGTACAGTACAAT...GCTGAGCTTGTGGCAAGGC seq_14566

The letter frequencies

Counts of the letters in the unmatched sequences.

x <- apply(consensusMatrix(motif_dat$unmatched_seq), 1, sum)
x <- x[x != 0]
kable(data.frame(letter = names(x),
                 count = x,
                 count_per_seq = round(x/length(motif_dat$unmatched_seq),2),
                 row.names = 1:length(x)))

|letter | count| count_per_seq| |:------|------:|-------------:| |A | 466241| 154.69| |C | 213997| 71.00| |G | 241376| 80.08| |T | 266341| 88.37| |+ | 8| 0.00|

Normalized counts of the letters in the unmatched sequences.

x_freq <- round(x/sum(x), 4)
kable(data.frame(letter = names(x_freq),
                 count = x_freq,
                 row.names = 1:length(x_freq)))

|letter | count| |:------|------:| |A | 0.3925| |C | 0.1801| |G | 0.2032| |T | 0.2242| |+ | 0.0000|

barplot(x/sum(x),
        main = 'Normalized counts of the letters\nin the unmatched sequences')

The sequence lengths

hist(width(motif_dat$unmatched_seq),
     main = "Histogram of the lengths of the unmatched sequences",
     xlab = "Sequence Length",
     ylab = "Number of Sequences")

philliplab/MotifBinner documentation built on Sept. 2, 2020, 11:41 a.m.